Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_007779438,44316.T54.2% 47.5 / 42.4 24coding (959/1863 nt)dxs1‑deoxy‑D‑xylulose‑5‑phosphate synthase
Reads supporting (aligned to +/- strand):  ref base . (7/4);  new base T (13/0);  total (20/4)
Fisher's exact test for biased strand distribution p-value = 3.11e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAGGTCGCGCATGTTCTTT  >  NC_007779/438197‑438604
                                                                                                                                                                                                                                                                      |                                                                                                                                                                      
tGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCg                                                                                                                                                                <  1:888564/250‑1 (MQ=255)
tGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCg                                                                                                                                                                >  1:486037/1‑250 (MQ=255)
  aTCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGCTTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGc                                                                                                                                                              >  2:760447/1‑250 (MQ=255)
   tCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCa                                                                                                                                                             >  1:367106/1‑250 (MQ=255)
    cATAGGCGCGTCGCATGAAAGTGGAGTAAATCGCGACCAGGTGTTCGCACCAACCAATCGCCAGACCCGCAGCACAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGCAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCaa                                                                                                                                                            <  2:932420/250‑1 (MQ=255)
        ggCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAAccg                                                                                                                                                        <  1:163986/250‑1 (MQ=255)
        ggCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAAccg                                                                                                                                                        <  2:251440/250‑1 (MQ=255)
          cgcgTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAAccgcc                                                                                                                                                      >  1:837258/1‑250 (MQ=255)
                                    gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCtac                                                                                                                            >  2:64941/1‑248 (MQ=255)
                                        cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCtactttt                                                                                                                        >  1:246724/1‑244 (MQ=255)
                                              gTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCtacttttcggcaa                                                                                                                  >  1:913151/1‑238 (MQ=255)
                                                                                                                        cGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCAGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGGTCGGGGCTTTTTCTGCCGGTTCATAAccgc                                                             >  2:429201/1‑248 (MQ=255)
                                                                                                                                    ttACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCAGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTgg                                                 >  2:816863/1‑250 (MQ=255)
                                                                                                                                                  gACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAgg                                   >  2:263183/1‑250 (MQ=255)
                                                                                                                                                   aCCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGTAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTTGTCATGATATGCAGGa                                  >  1:222975/1‑250 (MQ=255)
                                                                                                                                                         ccGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCg                            >  1:366329/1‑250 (MQ=255)
                                                                                                                                                             aaCCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGcc                        >  1:584929/1‑250 (MQ=255)
                                                                                                                                                              aCCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCt                       >  1:384099/1‑250 (MQ=255)
                                                                                                                                                                    aCGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAgg                 >  1:7830/1‑250 (MQ=255)
                                                                                                                                                                     cGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAGGt                >  1:572537/1‑250 (MQ=255)
                                                                                                                                                                        aTCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAGGTcgc             >  1:415333/1‑250 (MQ=255)
                                                                                                                                                                          cGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAGGTCgcgc           >  1:1017655/1‑250 (MQ=255)
                                                                                                                                                                           gCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAGGTCACGCa          >  2:547437/1‑250 (MQ=255)
                                                                                                                                                                                   aaTCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAGGTCGCGCATGTTCttt  >  1:891964/1‑250 (MQ=255)
                                                                                                                                                                                                                                                                      |                                                                                                                                                                      
TGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGTAGCGATCCGGGAATTTACGTGAAAACTCGACCATGCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAAAGTGATCGGGTCTTTTTCTGCCGGTTCATAACCACGACCTTTTTTGGTCATGATATGCAGGAACTGCGGGCCTTTCAGGTCGCGCATGTTCTTT  >  NC_007779/438197‑438604

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑